Chromosome engineering is the study of genetic modifications that affect large segments of chromosomes. Top down approaches start with pre-existing chromosomes and modify them in vivo by introducing, for instance, large deletions, inversions, or duplications. Bottom up approaches, on the other hand, attempt to design and build chromosomes de novo. In either case, we need a strong understanding not only of chromosomal features that confer mitotic stability, including centromeres, telomeres, and origins of replication, but also the effect of the spatial relationships of these elements with one another and with other chromosomal features like genes.
The Saccharomyces cerevisiae genome is an excellent platform to develop tools for chromosome engineering given the ease of genetic manipulation and similarity to higher eukaryotes. The S. cerevisiae genome is composed of 12 Mb of DNA inherited via 16 linear chromosomes ranging in size from 270 kb to over 1 Mb (1). Two important cis elements are required to maintain chromosome stability through mitosis and meiosis: compact point centromeres (˜125 bp) ensure faithful segregation of sister chromatids (2), and conserved telomere sequences protect the ends of each chromosome and guarantee the maintenance of chromosome length during replication (3, 4). With these elements intact, many lines of evidence indicate budding yeast tolerates a high degree of chromosomal modifications without affecting viability, for instance: (a) the largest yeast chromosome (IV) can be sub-divided into 11 separate mini-chromosomes (5); (b) more than 500 kb, including 247 non-essential genes, can be deleted in a single haploid strain (6); (c) any of the 16 chromosomes can be individually destabilized in a diploid cell to generate a chromosomal complement of 2n−1 (7); (d) a designer, synthetic chromosome arm, synIXR, was shown to power growth of budding yeast in the absence of the native chromosome sequence (8).